Individual differences in the acute response to drugs of abuse can influence future drug taking and may thus influence risk for drug abuse and addiction. Several lines of evidence indicate that genetic variation contributes to variability in the acute response to drugs of abuse. Recently developed genetic methodologies make it possible to identify the underlying genetic factors that govern these differences. We have already collected data from a large number of healthy human subjects, using highly controlled laboratory-based procedures to measure the acute subjective, behavioral, and physiological responses to d-amphetamine. We currently have DNA from 318 such subjects, and will have reached our goal of collecting 400 by the projected start date of this proposal. We have already examined a number of candidate genes using a targeted genotyping strategy that focuses on replicating genetic associations identified by other studies. In this proposal we seek to use a less biased genome-wide approach. Specifically, we will genotype these 400 subjects using the Affymetrix 6.0 array to obtain more than 900,000 single nucleotide polymorphisms (SNPs) as well as information about copy number variants (CNVs). We will approach the analysis of genotypes and phenotypes using a frequentist approach, a modified frequentist approach, and a Bayesian analysis. The first approach will use a standard genome-wide association analysis (GWAS), without any prior hypotheses about which SNPs or CNVs are most likely to be true positives. This approach is risky because our sample is relatively small for such a large number of tests. Nevertheless, the effect size of pharmacogenetic variants may be stronger than for disease traits, so our GWAS may identify genome-wide significant results. Our second approach will consider certain specific subpopulations of SNPs for which we believe there is a strong prior probability of a true positive. We delineate several such subpopulations and discuss their relative strengths and weaknesses. We will incorporate this information by using a weighted multiple testing procedure that facilitates the input of prior information (Roeder et al., 2006, 2007). This method enhances the power to detect associations at candidate loci with minimal loss in power to detect other associations. Our third approach will utilize Bayesian methods, as implemented in BIMBAM (Guan and Stephens 2008). By approaching this same problem with a different statistical framework we can directly estimate the strength of the evidence that a given marker is associated with response to amphetamine. This approach also allows us to account for specific subpopulations that we believe to be enriched for true positives. Our proposal is designed to leverage the substantial investment that has already been made in collecting and carefully phenotyping these 400 subjects. We are taking advantage of technical advances that have made it relatively inexpensive to obtain very large numbers of genotypes. Our statistical approach has the potential to identify SNPs that may contribute to both acute response, and perhaps also other clinically significant endpoints such as drug abuse and addiction. It combines a number of statistical tools to perform a sophisticated GWAS while accounting for other sources of information. We believe that our approach will maximize the potential to obtain new information from our unique sample. PUBLIC HEALTH RELEVANCE: Abuse of stimulant drugs like cocaine, amphetamine and methamphetamine are major public health problems. We are trying to identify genetic differences that influence differences in the response to d- amphetamine, in healthy young adults. About 70% of volunteers like the effects of amphetamine, but about 30% do not;multiple lines of evidence suggest that some of this variability is due to genetic differences. Studies have shown that people who like the effects of a drug continue taking them and are at increased risk for drug abuse. We hope that by identifying genes that influence drug liking we can predict risk of drug abuse and better understand the biological nature of drug abuse in susceptible and resistant people.